FFPE Pilot Phase II (FPPP) Samples Report
2016_07_15 Data Snapshot
Overview
Introduction

The Broad GDAC mirrors data from the DCC on a daily basis. Although all data is mirrored, not every sample is ingested into Firehose. There are three main mechanisms that filter samples to ensure that only the most scientifically relevant samples make it into our standard data and analyses runs. These three mechanisms are redactions, replicate filtering, and blacklisting. This report summarizes the data that is ingested into Firehose, describes the three filtering mechanisms, lists those samples that are removed, and gives all available annotations from the DCC's Annotation Manager.

Summary

There were 0 redactions, 0 replicate aliquots, 0 blacklisted aliquots, and 190 FFPE aliquots. The table below represents the sample counts for those samples that were ingested into firehose after filtering out redactions, replicates, and blacklisted data, and segregating FFPEs.

Table 1.  This table provides a breakdown of sample counts on a per sample type and, if applicable, per subtype basis. Each count is a link to a table containing a list of the samples that comprise that count and details pertaining to each individual sample (e.g. platform, sequencing center, etc.). Please note, there are usually multiple protocols per data type, so there are typically many more rows than the count implies.

Sample Type BCR Clinical CN LowP Methylation mRNA mRNASeq miR miRSeq RPPA MAF rawMAF
TP 38 38 0 0 0 0 0 0 23 0 0 0
TR 1 1 0 0 0 0 0 0 0 0 0 0
NB 37 37 0 0 0 0 0 0 0 0 0 0
NT 24 24 0 0 0 0 0 0 0 0 0 0
FFPE 0 0 0 0 0 0 0 0 22 0 0 0
Totals 38 38 0 0 0 0 0 0 23 0 0 0
FPPP Primary Solid Tumor BCR Data

Table S1. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-44-2656 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2662 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2665 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2666 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2668 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-3917 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-3918 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-4112 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-5645 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-6146 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-6147 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-6775 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-2674 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-2677 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-2684 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-3809 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-3810 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-5656 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-5659 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-6650 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-6780 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-6781 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A0DB Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A13D Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A13E Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A26E Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A26J Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-3923 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-3924 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-5633 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-5635 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BK-A0CA Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BK-A0CC Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BK-A139 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BK-A26L Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BL-A0C8 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BL-A13I Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BL-A13J Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
FPPP Primary Solid Tumor Clinical Data

Table S2. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-44-2656 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2662 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2665 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2666 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2668 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-3917 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-3918 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-4112 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-5645 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-6146 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-6147 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-6775 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-2674 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-2677 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-2684 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-3809 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-3810 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-5656 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-5659 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-6650 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-6780 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-6781 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A0DB Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A13D Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A13E Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A26E Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A26J Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-3923 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-3924 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-5633 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-5635 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BK-A0CA Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BK-A0CC Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BK-A139 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BK-A26L Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BL-A0C8 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BL-A13I Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BL-A13J Biospecimen Metadata - Complete Set NCH BCR 1 clinical
FPPP Primary Solid Tumor miRSeq Data

Table S3. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-44-6146-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-44-6146-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-44-6147-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-44-6147-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-44-6775-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-44-6775-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A6-5656-01A-21H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A6-5656-01A-21H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A6-6650-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A6-6650-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A6-6780-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A6-6780-01A-11H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A6-6781-01A-22H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A6-6781-01A-22H-A279-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A0DB-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A0DB-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A13D-01A-13R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A13D-01A-13R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A13E-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A13E-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A26E-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A26E-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A26J-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A26J-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-B2-3923-01A-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-B2-3923-01A-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-B2-3924-01A-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-B2-3924-01A-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-B2-5633-01A-01R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-B2-5633-01A-01R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-B2-5635-01A-01R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-B2-5635-01A-01R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BK-A0CA-01A-21R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BK-A0CA-01A-21R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BK-A0CC-01A-21R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BK-A0CC-01A-21R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BK-A139-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BK-A139-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BK-A26L-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BK-A26L-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BL-A0C8-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BL-A0C8-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BL-A13I-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BL-A13I-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BL-A13J-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BL-A13J-01A-11R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
FPPP Recurrent Solid Tumor BCR Data

Table S4. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-BK-A139 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
FPPP Recurrent Solid Tumor Clinical Data

Table S5. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-BK-A139 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
FPPP Blood Derived Normal BCR Data

Table S6. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-44-2656 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2662 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2665 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2666 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2668 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-3917 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-3918 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-4112 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-5645 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-6146 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-6147 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-6775 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-2674 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-2677 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-2684 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-3809 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-3810 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-5656 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-5659 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-6650 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-6780 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-6781 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A0DB Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A13D Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A13E Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A26E Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A26J Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-3923 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-3924 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-5633 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-5635 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BK-A0CA Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BK-A0CC Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BK-A139 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BK-A26L Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BL-A0C8 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BL-A13J Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
FPPP Blood Derived Normal Clinical Data

Table S7. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-44-2656 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2662 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2665 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2666 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2668 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-3917 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-3918 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-4112 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-5645 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-6146 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-6147 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-6775 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-2674 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-2677 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-2684 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-3809 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-3810 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-5656 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-5659 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-6650 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-6780 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-6781 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A0DB Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A13D Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A13E Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A26E Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A26J Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-3923 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-3924 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-5633 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-5635 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BK-A0CA Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BK-A0CC Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BK-A139 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BK-A26L Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BL-A0C8 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BL-A13J Biospecimen Metadata - Complete Set NCH BCR 1 clinical
FPPP Solid Tissue Normal BCR Data

Table S8. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-44-2656 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2662 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2665 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-2668 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-3918 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-4112 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-5645 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-6146 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-6147 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-44-6775 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-2674 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-2677 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-2684 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-3809 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-3810 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A6-5659 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A0DB Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-A7-A13E Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-3923 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-3924 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-5633 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-B2-5635 Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BL-A13I Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
TCGA-BL-A13J Biospecimen Metadata - Complete Set NCH BCR 1 biospecimen
FPPP Solid Tissue Normal Clinical Data

Table S9. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-44-2656 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2662 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2665 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-2668 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-3918 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-4112 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-5645 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-6146 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-6147 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-44-6775 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-2674 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-2677 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-2684 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-3809 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-3810 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A6-5659 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A0DB Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-A7-A13E Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-3923 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-3924 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-5633 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-B2-5635 Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BL-A13I Biospecimen Metadata - Complete Set NCH BCR 1 clinical
TCGA-BL-A13J Biospecimen Metadata - Complete Set NCH BCR 1 clinical
FPPP FFPE miRSeq Data

Table S10. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-44-6146-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-44-6146-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-44-6147-01B-06R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-44-6147-01B-06R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-44-6775-01C-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-44-6775-01C-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A6-5656-01B-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A6-5656-01B-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A6-6650-01B-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A6-6650-01B-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A6-6780-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A6-6780-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A6-6781-01B-06R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A6-6781-01B-06R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A0DB-01C-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A0DB-01C-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A13D-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A13D-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A13E-01B-06R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A13E-01B-06R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A26E-01B-06R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A26E-01B-06R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-A7-A26J-01B-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-A7-A26J-01B-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-B2-3923-01B-10R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-B2-3923-01B-10R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-B2-3924-01B-03R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-B2-3924-01B-03R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-B2-5633-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-B2-5633-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-B2-5635-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-B2-5635-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BK-A0CA-01B-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BK-A0CA-01B-02R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BK-A0CC-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BK-A0CC-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BK-A26L-01C-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BK-A26L-01C-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BL-A0C8-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BL-A0C8-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BL-A13I-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BL-A13I-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-BL-A13J-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-BL-A13J-01B-04R-A27D-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression

The sample type short letter codes in the table above are defined in the following list.

  • TP: Primary Solid Tumor

  • TR: Recurrent Solid Tumor

  • TB: Primary Blood Derived Cancer - Peripheral Blood

  • TAP: Additional - New Primary

  • TM: Metastatic

  • TAM: Additional Metastatic

  • NB: Blood Derived Normal

  • NT: Solid Tissue Normal

  • NBC: Buccal Cell Normal

  • NBM: Bone Marrow Normal

The following platforms are outdated and are not included in the counts depicted in the table above.

  • Agilent SurePrint G3 Human CGH Microarray Kit 1x1M

  • Agilent Human Genome CGH Microarray 244A

  • Agilent Human Genome CGH Custom Microarray 2x415K

  • Affymetrix Human Exon 1.0 ST Array

  • Illumina DNA Methylation OMA002 Cancer Panel I

  • Illumina DNA Methylation OMA003 Cancer Panel I

  • Illumina Human1M-Duo BeadChip

  • Illumina 550K Infinium HumanHap550 SNP Chip

Figure 1.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

Results
FFPE Cases
Additional Annotations from the DCC's Annotations Manager
Methods & Data
Redactions and Other Annotations

Annotation data was taken from theTCGA Data Portalusing the query string:

https://tcga-data.nci.nih.gov/annotations/resources/searchannotations/json?item=TCGA

Redaction information was generated by filtering for the annotationClassificationName "Redaction"

FFPE information was generated by filtering for "FFPE" in annotation note text

Additional FFPEs were garnered from clinical data

Remaining annotations were sorted into sections by annotationClassificationName

Preprocessors
mRNA Preprocessor

The mRNA preprocess median module chooses the matrix for the platform(Affymetrix HG U133, Affymetrix Exon Array and Agilent Gene Expression) with the largest number of samples.

mRNAseq Preprocessor

The mRNAseq preprocessor picks the "scaled_estimate" (RSEM) value from Illumina HiSeq/GA2 mRNAseq level_3 (v2) data set and makes the mRNAseq matrix with log2 transformed for the downstream analysis. If there are overlap samples between two different platforms, samples from illumina hiseq will be selected. The pipeline also creates the matrix with RPKM and log2 transform from HiSeq/GA2 mRNAseq level 3 (v1) data set.

miRseq Preprocessor

The miRseq preprocessor picks the "RPM" (reads per million miRNA precursor reads) from the Illumina HiSeq/GA miRseq Level_3 data set and makes the matrix with log2 transformed values.

Methylation Preprocessor

The methylation preprocessor filters methylation data for use in downstream pipelines. To learn more about this preprocessor, please visit the documentation.